The affair caused a flurry of press speculation that United, who won the title last Sunday, might have points deducted for breaking Premier League rules.
The Premier League (FAPL) cleared the clubs but today Manchester United club sought to justify their actions.
In the contract turning Howard's loan move to Everton into a permanent transfer in January, United wanted to insert a clause that would have prevented him from playing when the two sides met at Goodison Park on April 28.
The Premier League did not permit such a clause and the 28-year-old American was not selected because of a gentlemen's agreement between the two clubs.
His replacement, Iain Turner, then made an error which allowed United to score and go on to secure a 4-2 win, opening a five-point lead over title chasers Chelsea.
''At no point did either club set out to break FAPL rules,'' United said in a statement.
''The transfer of Tim Howard, who was then on a season-long loan to Everton, reflected Everton's desire to acquire the player, the player's wish to secure his long-term future and Manchester United's willingness to sell him.
''In drafting the transfer agreement with Everton's approval, the club inserted a clause acknowledging that Tim Howard would not be available for selection against United,'' the club said.
''It remains both the clubs' position that such a deal could not be a ''material influence'' on the integrity of the 2006/07 FAPL season if it reflects no change to the situation as it existed at the time.
''Before the deal, Tim Howard was not able to play against Manchester United. After the deal, the same would have been true. It therefore would have had no effect on the integrity of the competition whatsoever.
''The FAPL rejected the inclusion of this in the contract.'' While exclusion clauses are common in loan deals they are against Premier League rules for permanent transfers.
The clause was not included and the Premier League cleared United of contravening their rules.
REUTERS AKD HT1955